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5.0.16 (#223)
* README update * CHANGELOG update * decontainer setup * Inline nginx and Varnish config templates into docker-compose.yml SaxonJS 3 bump to beta-2 * ssl_verify_client fix * Removed user-supplied `dct:created` values * CHANGELOG update * Fixed XSLT SEF generation in Maven build * Removed comment * [maven-release-plugin] prepare release linkeddatahub-5.0.15 * [maven-release-plugin] prepare for next development iteration * Javadoc fixes * Updated CHANGELOG * More Javadoc fixes * Comment fix
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‎CHANGELOG.md‎

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## [5.0.16] - 2025-06-15
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## Added
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- Javadoc comments
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## [5.0.15] - 2025-06-15
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### Changed
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- Inlined nginx and Varnish config templates into `docker-compose.yml`
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- SaxonJS 3 bump to 3.0.0-beta-2
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### Fixed
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- Remove user-supplied `dct:created` values to prevent timestamp conflicts
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- XSLT SEF generation in Maven build
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## [5.0.14] - 2025-05-25
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### Added
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- Inline chart save feature for better user experience
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### Changed
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- Improved template match patterns for better performance
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### Fixed
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- Fixed action URL in navbar form
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- Comment fixes in codebase
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## [5.0.13] - 2025-05-12
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### Added
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- Saxon-JS upgraded from 2.x to 3.x with "suspended promise tree" architecture
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- Auto-generation of WebID certificates (owner and secretary) in entrypoint
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- Request access modal forms with ACL integration
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- Multi-platform Docker images (ARM64 + AMD64) with GitHub Actions
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- Modal document editing forms with in-place editing
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- Rate limiting and retry logic for HTTP 429 responses with `Retry-After` headers
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- Conditional HTTP requests support (`ETag`, `If-None-Match`, preconditions)
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- Access control endpoints for authorization management
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- Progress indicators for long-running operations
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- Drag-and-drop improvements for block reorganization
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- SPARQL endpoint read-only access for authenticated agents
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- Enhanced form controls with better `datetime-local` rendering
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- New HTTP test suite for conditional requests and access endpoints
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- Chart creation workflow improvements
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- View system overhaul - `ldh:View` now embedded via `ldh:Object`
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- Secrets management for Google OAuth credentials
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- Enhanced SSL/TLS management with automated keystore generation
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- MacOS compatibility improvements
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### Changed
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- CLI tools reorganization - scripts moved to `bin/` directory with PATH management
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- Client-side named templates converted to XPath functions for better composability
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- Promise-based rendering for charts, views, and objects
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- `ldh:View` is now a "normal" resource instead of content block
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- Authorization query optimization for better performance
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- Document type injection with dynamic `VALUES` for type-based queries
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- Varnish configuration improvements with separate VCL templates
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- User-specific content handling with proper cache bypass
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- RDF/POST parser improvements for empty values and relative URIs
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- SPARQL.js 2.x compatibility with regex fixes for datatype URIs
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- Container orchestration with memory limits and better configuration
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- Base image updates: `atomgraph/letsencrypt-tomcat:10.1.34`, `atomgraph/fuseki:4.7.0`
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- XHTML namespace handling with default `xmlns="http://www.w3.org/1999/xhtml"`
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- Block system improvements with better nesting and unique identifiers
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- Authorization filter improvements with `SERVICE`-less queries
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- Static file optimizations with increased burst limits
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### Fixed
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- Multiple null pointer exceptions in Java code
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- XPath syntax errors in XSLT stylesheets
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- Variable naming conflicts and scoping issues
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- Certificate permission issues across platforms
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- Progress bar visibility and selector issues
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- Block rendering and nesting logic
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- Form submission and response handling
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- Chart rendering and display logic
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- View navigation and object loading
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- HTTP status code handling (`201 Created`, `308 Permanent Redirect`)
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- Double slash URI prevention in requests
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- Container CSS and modal sizing issues
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- RDFS-specific vocabulary support
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### Removed
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- `IMPORT_KEEPALIVE` parameter
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- Unused `Reserialize` Saxon function (replaced with pure XSLT)
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- Debug output from XSLT stylesheets
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- Unnecessary `ixsl:http-request` arguments
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- Secret environment variables from Dockerfile
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- `bs2:RowContent` mode in XSLT
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## [4.0.10] - 2024-11-07
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### Changed
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- Fixed namespace prefix declaration in client-side XSLT

‎CLAUDE.md‎

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# CLAUDE.md
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This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
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## Project Overview
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LinkedDataHub (LDH) is a low-code Knowledge Graph application platform that enables managing data, creating visualizations, and building apps on RDF Knowledge Graphs. It's a completely data-driven platform where applications and documents are defined as data, managed using a single generic HTTP API, and presented using declarative technologies.
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## Build System and Development Commands
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LinkedDataHub uses Maven as the primary build system with Docker for containerization.
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### Development Setup
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```bash
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# Initial setup (requires .env file configuration)
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./bin/server-cert-gen.sh .env nginx ssl
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docker-compose up --build
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```
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### Core Build Commands
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```bash
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# Maven build (Java 17 required)
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mvn clean install
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# Build specific profiles
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mvn -Pstandalone clean install # Standalone WAR
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mvn -Pdependency clean install # JAR dependency
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mvn -Prelease clean install # Release with signing
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# Docker-based development
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docker-compose up --build # Start all services
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docker-compose down -v # Stop and remove volumes
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sudo rm -rf data uploads && docker-compose down -v # Complete reset
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```
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### Testing
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```bash
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# HTTP tests (requires running application)
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cd http-tests
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./run.sh ssl/owner/cert.pem [password] ssl/secretary/cert.pem [password]
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# Test individual suites
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find ./document-hierarchy/ -name '*.sh' -exec bash {} \;
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```
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## Architecture Overview
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### Core Application Structure
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- **JAX-RS based**: Uses Jersey framework for RESTful web services
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- **Multi-application architecture**: Separate admin and end-user applications
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- **Data-driven design**: Applications and resources defined as RDF data
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- **XSLT-based UI**: Client-side rendering using Saxon-JS with XSLT transformations
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### Key Components
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#### Applications (`com.atomgraph.linkeddatahub.apps.model`)
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- `AdminApplication` - Administrative interface and functions
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- `EndUserApplication` - Main user-facing application
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- Applications are data-driven and loaded from RDF datasets
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#### Security & Authentication (`com.atomgraph.linkeddatahub.server.filter.request.auth`)
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- WebID-based authentication with client certificates
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- OAuth2 integration (Google)
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- Authorization filters and context management
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- Multi-level security: Agent, Authorization, and Application filters
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#### Data Management (`com.atomgraph.linkeddatahub.model`)
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- RDF-native data handling with Jena
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- Import/Export functionality for CSV, RDF, and other formats
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- SPARQL endpoint integration with separate admin and end-user stores
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#### Resource Handling (`com.atomgraph.linkeddatahub.resource`)
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- RESTful resource endpoints for CRUD operations
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- File upload and content-addressed storage
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- Transformation and generation utilities
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### Service Architecture
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The application runs as a multi-container setup:
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- **nginx**: Reverse proxy and SSL termination
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- **linkeddatahub**: Main Java application (Tomcat)
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- **fuseki-admin/fuseki-end-user**: Separate SPARQL stores
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- **varnish-frontend/varnish-admin/varnish-end-user**: Caching layers
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### Data Flow
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1. Requests come through nginx proxy
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2. Varnish provides caching layer
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3. LinkedDataHub application handles business logic
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4. Data persisted to appropriate Fuseki triplestore
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5. XSLT transforms data for client presentation
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### Key Extension Points
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- **Vocabulary definitions** in `com.atomgraph.linkeddatahub.vocabulary`
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- **Custom resource handlers** in `com.atomgraph.linkeddatahub.resource`
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- **Import processors** in `com.atomgraph.linkeddatahub.imports`
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- **XSLT transformations** in `src/main/webapp/static/com/atomgraph/linkeddatahub/xsl`
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## CLI Tools
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LinkedDataHub includes extensive CLI tools in the `bin/` directory:
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- Resource management: `create-container.sh`, `create-item.sh`, `get.sh`, `post.sh`, `put.sh`
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- Import functionality: `imports/create-csv-import.sh`, `imports/import-rdf.sh`
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- Admin operations: `admin/model/add-class.sh`, `admin/acl/create-authorization.sh`
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- Certificate management: `webid-keygen.sh`, `server-cert-gen.sh`
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Add CLI tools to PATH for development:
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```bash
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export PATH="$(find bin -type d -exec realpath {} \; | tr '\n' ':')$PATH"
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```
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## Development Notes
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- Java 17 is required for compilation
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- The application uses AtomGraph's Processor and Web-Client libraries as core dependencies
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- XSLT stylesheets are processed during build to inline XML entities
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- Saxon-JS SEF files are generated during Maven package phase for client-side XSLT
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- WebID certificates are required for authenticated API access
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- The system expects Jena CLI tools to be available (`JENA_HOME` environment variable)

‎README.md‎

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- `data` where the triplestore(s) will persist RDF data
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- `datasets` where LDH persists agent metadata files
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- `uploads` where LDH stores content-hashed file uploads
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It should take up to half a minute as datasets are being loaded into triplestores. After a successful startup, the last line of the Docker log should read something like:
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```
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linkeddatahub_1 | 09-Feb-2021 14:18:10.536 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [32609] milliseconds
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```
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It should take up to half a minute as datasets are being loaded into triplestores. After a successful startup you should see periodic healtcheck requests being made to the https://localhost:4443/ns URL.
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6. Install `ssl/owner/keystore.p12` into a web browser of your choice (password is the `owner_cert_password` secret value)
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- Google Chrome: `Settings > Advanced > Manage Certificates > Import...`
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- Mozilla Firefox: `Options > Privacy > Security > View Certificates... > Import...`
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export PATH="$(find bin -type d -exec realpath {} \; | tr '\n' ':')$PATH"
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```
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If you will be using LinkedDataHub's CLI regurarly, add the above command to your shell profile.
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_:warning: The CLI scripts internally use [Jena's CLI commands](https://jena.apache.org/documentation/tools/). Set up the Jena environment before running the scripts._
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